Bio Saga Blog - A Chronicle of Life Sciences & Informatics

              Know About Our Workshop On Bioinformatics and Protein Structure Prediction 10th to 12th May 2019 | Pune, India | 09:30 AM - 05:00 PM Our 3 day comprehensive workshop on Bioinformatics and Protein Structure Prediction aims at providing systematic Hands-on-Training on Protein visualization, mutation & other manipulations.Understand concept of in-silico protein modelling using servers & software’s.Understanding concept of protein motif and domains.Understanding concept of protein structure prediction by Modeller COMPREHENSIVE & SEQUENTIAL SESSIONS ON: ▪ Introduction to Biological databases ▪ Multiple Sequence Alignment – CLUSTALW ▪ Introduction to Proteins & Protein Databases-UNIPROT ▪ Study of proteins and their structures ▪ Protein Secondary Structure Prediction tools ▪ Protein Tertiary Structure Prediction using Servers & Modeller ▪ Protein Structure Validation ...

Two-day national-level workshop on Protein Structural Analysis & Homology Modelling DATES: October 23-24, 2010 LOCALE: Department of Biotechnology and Bioinformatics,  Padmashree Dr. D. Y. Patil University Sector 15, CBD,  Belapur, Navi Mumbai-400614, India Janu Ganak and the Bioinformatics Community of the Department of Biotechnology and Bioinformatics, Padmashree Dr. D Y Patil  University, are pleased to inform you that a two day workshop on "PROTEIN STRUCTURAL ANALYSIS AND HOMOLOGY  MODELLING" is being organized.  This workshop is the second of a series of workshops that are aimed at  giving complete  hands-on experience in various tools and techniques  used  in the fields of life science and bioinformatics. This workshop is aimed at giving practical experience on the basic methods of visualization, analysis and modeling of protein structures using bioinformatics tools.  Both under-graduate...

"Protein Structure and Drug Discovery" Workshop – Sept 30th to Oct 1st 2010 La Jolla, CA. Please join us at MolSoft's (   www.molsoft.com   ) "Protein Structure and Drug Design" Workshop in La Jolla, California USA. For more information and a registration form see:   www.molsoft.com/training.html This workshop is suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate. The workshop is presented by Prof. Ruben Abagyan (University of California San Diego) and Dr. Maxim Totrov (MolSoft). Price: $349 (Academics) $749 (Commercial) The workshops will consist of lectures, demonstrations, and "hands-on" computational experiments and will cover the following topics: - How To Display Fully Interactive 3D Molecules in PowerPoint and the Web - Sequence and Protein Structure Analysis - Protein Modeling and Simulations - Structure...

Bioinformatics firm Biosof said today that it is working with IBM to provide a server platform for its PredictProtein product for analyzing protein structure and function. The collaboration will enable Biosof’s customers to use ProteinPredict through a virtual private network or on-site installation while running IBM’s high-performance computing hardware, New York-based Biosof said in a statement. “Working with IBM provides our customers the unique opportunity to combine a secure infrastructure and cutting-edge hardware needed to run our highly resource-intensive algorithms,” said Burkhardt Rost, a manager of Biosof. Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are ...

Here is a abstract that i had submitted at the Plant & Animal Genomes XI Conference January 11-15, 2003 Town & Country Convention Center San Diego, CA. I do not know how relevant is the issue to this day. If any one is interested or if any one is working in these lines, do let me know also pour in your suggestions and comments if any. Fiber quality in cotton is one very vital trait demanding international focus in both scientific and commercial arena. Phytohormones play a major role in all cellular processes in plant development. We have focused our study on the influence of phytohormones in improving the staple length of cotton fiber. There are several pathways, which influence staple length in cotton, among which we have concentrated on the expression pattern of Lipid Transfer Protein3. A cotton fiber protein gene Ltp3, Lipid transfer protein3 (coding for a LTP3 protein), is specifically expressed in fibers at high levels, during the elongation stage. Its levels reach a maxim...

Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details. Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space. Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length. Do you want to know more?

Here is a abstract that i had submitted at the 3D sig:Structral Bioinformatics at the 1st Structural Bioinformatics Meeting at ISMB 29-30 July 2004, Glasgow, Scotland, UK. I do not know how relevant is the issue to this day. I am interested in working further in this area and i am interested in collaborating. Do let me know your comments also pour your suggestions on how to further this study. In silico methods can be used to design protein, based on stability and functionality using computational methods rather than laboratory procedures (Comet et al., 2000). The changes taking place due to the transfer of motif region from human Catechol-O-methyltansferase to rat Catechol-O-methyltransferase can be studied effectively using computational methods. This will provide insight for further development of the study about the function of neurotransmitter region of catechol-O-methyltransferase and its involvement in the Parkinson’s disease. Catechol-O-methyltransferase (COMT) catalyzes the t...

Many of you involved in structure based drug discovery will know very well about the numerous problems and errors in the data found in the Protein Data Bank (PDB) especially concerning the ligand structures. There have been a lot of publications about such errors, e.g. in Jones et al. J Mol. Biol. (1997) 267 :727, and I heard various conference presentations about this topic too, e.g. by Gerard Kleywegt (University of Uppsala), titled “Protein crystallography: not as simple as ABC then?” at Bryn Mawr, Philadelphia (15-19 October 2007) eChemInfo meeting . The errors are often blamed on the low resolution of the structures involving large protein structures (often thousands of atoms). One would assume that the small molecule crystal structures of the Cambridge Structural Database ( CSD ) do not have such errors, since they have much higher resolution and dealing with small molecules. Let me correct that wrong assumption! Do you want to know more?

Scientists at the U.S. Department of Energy's (DOE) Argonne National Laboratory have determined the structure of a key protein domain in a bacterium that could help with bioremediation of uranium-contaminated land sites. The researchers, led by Argonne senior biophysicist Marianne Schiffer, characterized the structure of one of the principal domains in a protein responsible for certain types of movement exhibited by the bacterium Geobacter sulfurreducens. Geobacter lives in predominantly low oxygen environments and generates energy by transferring electrons to various metallic electron-accepting atoms such as iron or uranium. This ability suggests that Geobacter might be used for remediation of certain types of hazardous waste. For example, when uranium is reduced by this process to its insoluble form, it no longer leaks into groundwater and engineers can inexpensively remove the precipitated uranium. Do you want to know more?

Already blogging about vital information that can be obtained form publications and scientific literature Smart tools to track, analyze and visualize research and the importance of Protein structure information in Protein structure databases with new web services for structural biology and biomedical research . Now one of the tactics used by influenza virus to take over the machinery of infected cells has been laid bare by structural biologists at the European Molecular Biology Laboratory ( EMBL ) and the joint Unit of Virus Host-Cell Interaction of EMBL, the University Joseph Fourier and National Centre for Scientific Research (CNRS), in Grenoble, France. The high-resolution image of the influenza virus' PB2 protein shows how the virus steals a 'cap' molecule from its host to take over the protein production machinery and multiply. PB2 binds the cap by sandwiching it between aromatic amino acids. "Viruses are masters of cunning when it comes to hijacking the normal f...

Brookhaven Lab researchers Subramanyam Swaminathan, Desigan Kumaran and Richa Rawat. "We have found a highly efficient inhibitor of botulinum neurotoxin type A - the most potent of seven neurotoxins produced by the bacterium Clostridium botulinum. This finding can lead to a very effective drug to stop the devastating effects of the toxin," said Dr. Subramanyam Swaminathan, Botulinum neurotoxin -- responsible for the deadly food poisoning disease botulism and for the beneficial effects of smoothing out facial wrinkles - can also be used as a dreaded biological weapon. When ingested or inhaled, less than a billionth of an ounce can cause muscle paralysis and eventual death. Although experimental vaccines administered prior to exposure can inhibit the destructive action of this neurotoxin - the most deadly protein known to humans -- no effective pharmacological treatment exists. Scientists have now taken the first step toward designing an effective antidote to the most potent ...

The Protein Data Bank Japan (PDBj) curates , edits and distributes protein structural data as a member of the worldwide Protein Data Bank (wwPDB) and currently processes 25–30% of all deposited data in the world. Structural information is enhanced by the addition of biological and biochemical functional data as well as experimental details extracted from the literature and other databases. Several applications have been developed at PDBj for structural biology and biomedical studies : (i) a Java-based molecular graphics viewer, j V; (ii) display of electron density maps for the evaluation of structure quality; (iii) an extensive database of molecular surfaces for functional sites, e F-site, as well as a search service for similar molecular surfaces, e F-seek; (iv) identification of sequence and structural neighbors; (v) a graphical user interface to all known protein folds with links to the above applications, Protein Globe. Recent examples are shown that highlight the...